What kind of cookie? I think cookies are pretty forgiving. I frequently use white whole wheat flour to no ill effect. Regular whole wheat flour might make it a little denser, but depending on what kind of cookie it is, it could still be good.

Whole wheat pastry flour will have more protein than white pastry flour, so they will be more dense. Are you looking to replace the wwpf entirely? If so, just use white pf and perhaps 1/8 cup or so more of it.

Are you looking for whole wheat or a fiber rich flour? I have done extensive research and testing with alternate flours, both high fiber and gluton-free. My tests have shown that if you use whole wheat pastry flour in a recipe it can be no more thatn 1/3 of the total flour amount. Meaning you gave to add 2/3 of AP flour. I wish there was a way to use all fiber-rich flours but unfortunately you will always need AP or Xantham Gum to alternate flours provide the gluton needed for baked goods.

I'm not a terribly experienced baker, but I've made many cookies and quick breads with only whilte whole wheat flour or whole wheat pastry flour. I don't even know what Xanthan Gum is. Maybe for a cake you need to use a mix with AP?

I am sorry, I should explain that Xantham gum is what you use to replce the gluton in flours that have none. You require a tiny amount...say about 1/4 tsp for each cup of gluton-free flour. Nowadays, with all the gluten-free adversities out there (almost like an allergy) people need to know how to make GF flours for subs for baked goods we have taken for granted our whole lives. Anyone with a blog of baking, should start to recognize the need to include gluten-free recipes.

I've baked with a number of her cookie recipes. She regularly specifies whole grain flours and I've never had a batch turn out thick or heavy, unless they were meant to, i.e. in the Carrot Oatmeal Cookies recipe.

For example, the Swedish Rye Cookies, are a combination of rye and whole wheat pastry flour...they were the most tender, delicate cookies...a similar cookie genre to the recipe you want to use. I'd say give the original recipe a try if you have access to whole wheat pastry flour.